The CIA’s growing suspicion of the colonel’s operations leads to a Green Beret (elite high-risk operatives) captain, Terry Crodelle, assigned to the case. Crodelle’s first salvo against the colonel is sending a team to Hao’s house to whisk Hao away for questioning at the Armed Forces Language School in Saigon. At first, Hao is happy Kim wasn’t home when he was taken, suggesting she is safe, but when he spots his wife in the building, Hao understands the gravity of the situation. Crodelle joins Hao and asks him about the operations planned by the colonel and Trung, telling Hao that he has picked the wrong friend in the colonel.

Hao understands the veiled threat and realizes he has no choice but to betray the colonel. Hao tells Crodelle that he supports all Americans and simply wants to emigrate to Singapore with his wife. Crodelle responds that if Hao cooperates with them, they can get him to Malaysia, a far better option. Hao is let go, but feels morally compromised, wondering if he should tell Trung that the Americans have intel on him. He arrives home, relieved to see Kim there.

Hiding his interrogation by Crodelle from the colonel, Hao escorts Trung, Ming, and the colonel to Skip’s villa. After making introductions, the colonel asks Skip to step outside so he can give him the bad news that Skip’s mother, Beatrice, has died of complications during a radical hysterectomy. The colonel’s words strike Skip “like a blow to the chest” (380). The colonel apologizes for bringing the news late; he received a cable from America three days ago but only read it today. The colonel was distracted as Johny Brewster (Crodelle’s boss) has passed orders to disband the Echo Company. Skip can attend Beatrice’s funeral in America if he likes. Skip refuses and humorlessly refers to himself as the colonel’s “orphan nephew.” The colonel assures Skip he will always have a family in the colonel.

Back at the villa, Hao reflects that his feelings about the colonel have changed since the meeting with Crodelle, with Hao now feeling afraid of the colonel. As Skip composes himself and returns inside, the colonel tells Skip to absorb all the information Trung can give him. While the others converse, a conflicted Hao wants to shout out that he is lying to everybody.

After the colonel and the others leave, Trung offers Skip his condolences about Beatrice, telling Skip that his own mother passed away in 1964. Skip thanks Trung for his commiserations and asks why Trung would betray his cause. Trung replies that the betrayal pains him, but he has realized that communism did not keep the promises it made. Since a grieving Skip cannot sleep, Trung stays up with him all night, talking. Skip thinks that he had conceived of Trung as a “Judas,” a betrayer, but Trung is more like Christ. The next day, Hao brings a message for Skip, indicating Voss wants to meet him in Saigon. Skip leaves Trung at his villa, assuring him he is safe there.

Meanwhile, the German assassin who killed Father Carignan arrives in Saigon for a new assignment. His name is revealed to be Dietrich Fest. Fest and Skip spot each other in Saigon. Fest wants to talk to Skip, but Skip walks away from him. Later, Fest meets the contacts who are to give him the details of his target. The contacts are members of Crodelle’s team. The men tell Fest they don’t have the exact specifics on his target yet, but will drop more information soon.

Skip and Voss catch up over lunch, where Skip learns that Voss’s daughter Celeste is now four years old. They are soon joined by Crodelle, an obvious ambush about which Voss did not tell Skip. Crodelle introduces himself to Skip as an officer from the “Regional Security Center.” He interrogates Skip about the colonel’s unpublished article in Intelligence Studies, calling its premise tricky and incendiary. Crodelle tells him the colonel is under the scanner for his dubious actions, such as taking command of the Echo Platoon at Cao Phuc and killing a VC without authorization. The colonel is not even supposed to be in Vietnam, having been recalled to the CIA headquarters at Langley weeks ago. Skip refuses to corroborate any of the information or reveal the content of the colonel’s index cards and walks out.

Back at the villa, Skip finds the colonel waiting for him, looking haggard and breathless. The colonel tells Skip that Trung has been moved from the villa, and Skip’s role in the operation is over because Skip betrayed the colonel. The colonel knows Skip met Crodelle today and revealed information about the colonel’s operations. The colonel’s life is a mess, with his wife in the US having filed for divorce. He cannot risk another betrayal from his family.

Shocked by the colonel’s accusations, Skip reassures him that he has not revealed anything to Crodelle. In fact, he has information for the colonel: Fest’s presence in Saigon. The news of Fest’s arrival makes the colonel all the more agitated, confirming to him that something bad is underway. As Skip promises his uncle that he loves him, the colonel refuses to believe that Skip is loyal, since love and loyalty are not the same thing.

After this distressing incident, the colonel disappears. Two weeks later, Skip receives a note from Jimmy Storm that the colonel is dead, his body found with his fingers and toes broken, indicating he was tortured. Skip is in disbelief. Over the next few days, stories float about the manner of the colonel’s death, ranging from the colonel being stabbed by a sex worker to being assassinated by the enemy.

As if things are shutting down one by one, Skip receives a letter from Kathy, through which she ends their affair. Kathy tells Skip that, torn between her desire for him and her spiritual calling, she has chosen the spiritual path. Skip also receives a letter from his mother’s pastor stating that Beatrice grew more spiritual in her last days, preparing herself for the end. The pastor includes Beatrice’s last letter to Skip, which contains an elegiac poem by William Carlos Williams. Skip feels the women in his life have bid him goodbye.

Skip spends the next few days looking over the colonel’s notes. In one of the cards, he finds the origin of the phrase “Tree of Smoke”: The colonel has noted a few passages from the Bible alluding to it, including the “‘palm trees of smoke” from the Book of Joel. Skip decides to compose a detailed, researched article on the colonel for Intelligence Studies, hoping to provide a deeper glimpse into his life. Skip finally learns the truth about the colonel’s escape from the Japanese. It is the same story that the colonel confided in Minh.

Months after the colonel’s death, Skip receives another summons for lunch with Voss. In Saigon, Voss confesses that it was he who passed on the colonel’s article to his superiors, hoping to curry favor with them. Voss apologizes for the error, and Skip forgives him. However, Voss says the article has set a certain chain of events in motion, which cannot be reversed. He himself is being sent back to the US, while Skip is to take a polygraph test with Crodelle. Skip agrees and goes to the language school with Voss, but tricks Voss and Crodelle and makes his escape to the villa.

Days later, he gets a visit from Jimmy. Jimmy tells him that Voss is dead, his helicopter shot down. Jimmy hits Skip, blaming him for the mess, though he can’t exactly say how Skip caused Voss’s death. Jimmy is also angry at the colonel, whom he thinks faked his death to carry out another covert operation. Skip suddenly recalls spotting Hao at the language school and realizes it is Hao who has been leaking information to the CIA. Skip is angry at Hao, but also understands that the man is doing what he has to in order to survive.

A few days after Jimmy’s visit, Crodelle shows up at Skip’s villa to offer Skip a final chance to cooperate with him. All Crodelle wants is for Skip to share the colonel’s files with him and exonerate himself. Skip pretends to agree and leads Crodelle up the stairs to the filing cabinets. With Crodelle distracted by staring at the cabinets, Skip points a gun at him, forcing him into a chair. Skip ties up Crodelle, takes all the colonel’s files outside, and burns them with the help of Mr. Tho. When Skip goes back in, Crodelle tells him that since Skip has burned all the evidence of the colonel’s treason himself, people will pin the blame for the colonel’s dubious operations on Skip. Skip ignores Crodelle, takes his car keys, and drives away.

Fest’s target is none other than Trung. Fest has been instructed to kill Trung at a specific date and time, which makes Fest uneasy. The specificity of the details means Fest himself is at risk. However, he watches Trung in the safe house where he is being kept, so he can study his movements. Learning that Trung goes out for dinner at a particular time, Fest decides that is the time he will gain entry into Trung’s room and wait for him.

The day of Trung’s planned murder, Jimmy arrives at Trung’s apartment—via a path which is not visible to an outsider—with a message from Hao that an assassin will soon arrive to kill him, though Jimmy thinks Hao is working for Crodelle. Jimmy and Hao make plans on how to tackle the assassin or assassins if they do show up. That evening, Trung leaves his room as usual, wondering if Hao’s warning is a trap. Fest enters Trung’s room as he had planned, but is ambushed by Jimmy. Jimmy pushes Fest down the stairs and kills him.